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Yorodumi- PDB-4zos: 2.20 Angstrom resolution crystal structure of protein YE0340 of u... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4zos | ||||||
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Title | 2.20 Angstrom resolution crystal structure of protein YE0340 of unidentified function from Yersinia enterocolitica subsp. enterocolitica 8081] | ||||||
Components | protein YE0340 from Yersinia enterocolitica subsp. enterocolitica 8081 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Yersinia enterocolitica subsp. enterocolitica 8081 / hypothetical protein YE0340 / CSGID / Center for Structural Genomics of Infectious Diseases | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Yersinia enterocolitica (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Halavaty, A.S. / Wawrzak, A. / Onopriyenko, O. / Grimshaw, S. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: To Be Published Title: 2.20 Angstrom resolution crystal structure of protein YE0340 of unidentified function from Yersinia enterocolitica subsp. enterocolitica 8081] Authors: Halavaty, A.S. / Wawrzak, A. / Onopriyenko, O. / Grimshaw, S. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4zos.cif.gz | 97.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zos.ent.gz | 74 KB | Display | PDB format |
PDBx/mmJSON format | 4zos.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4zos_validation.pdf.gz | 453.4 KB | Display | wwPDB validaton report |
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Full document | 4zos_full_validation.pdf.gz | 456.1 KB | Display | |
Data in XML | 4zos_validation.xml.gz | 16 KB | Display | |
Data in CIF | 4zos_validation.cif.gz | 22.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zo/4zos ftp://data.pdbj.org/pub/pdb/validation_reports/zo/4zos | HTTPS FTP |
-Related structure data
Related structure data | 1x7vS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
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-Components
#1: Protein | Mass: 12265.877 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Yersinia enterocolitica (bacteria) / Strain: Yersinia enterocolitica subsp. enterocolitica 8081 / Plasmid: pMCSG7-Halo / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL / References: UniProt: A0A0M3KL35*PLUS #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.5 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop Details: Crystallization: 20%Polyethylene Glycol 8000, 0.2M Sodium Chloride,Phosphate-Citrate Protein at 20 mg/ml |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 22, 2015 |
Radiation | Monochromator: Si(111) Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→30 Å / Num. obs: 18325 / % possible obs: 96.1 % / Redundancy: 3.7 % / Biso Wilson estimate: 31 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 16.5 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.337 / Mean I/σ(I) obs: 3.2 / % possible all: 90 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1X7V Resolution: 2.2→29.66 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.888 / SU B: 7.299 / SU ML: 0.192 / Cross valid method: THROUGHOUT / ESU R: 0.107 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.256 Å2
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Refinement step | Cycle: 1 / Resolution: 2.2→29.66 Å
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Refine LS restraints |
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